Ever thought that Kurama wanted Naruto to stay in the genjutsu to see into Hinata's mind as it pretained to Naruto? Naruto wasn't in any danger at that time but had he been in a dangerous situation at that time then Kurama would have broke him out. Naruto himself didn't even try breaking it and his skills are much higher than war arc Naruto. Except we don't know if Naruto wouldn't be able to break out of IT, Sasuke thought Naruto couldn't which doesn't make it a fact.
Think you forgot that a Naruto wasn't a perfect Jinchuuriki when he told Bee that nor did it show that Naruto even knew a perfect Jinchuuriki can breakout of genjutsus easily which Bee did which Edo Itachi's genjutsu (Itachi didn't even try using genjutsu after Bee broke out). So there is no manga facts saying perfect Jinchuuriki can't breakout of genjutsus. I don't see Sasuke putting a guy with 9 Bijuus in him in a genjutsu long enough to capitalize on it; also don't see him being able to enter Naruto's or Bee's consciousness to put their Bijuus in a genjutsu since it was said that Naruto reached a deeper level of conciousness after perfectly linking to Kurama when they finally became perfect Jinchuuriki so the same would be for Bee which is why Obito and Madara didn't try placing their Bijuus in genjutsus.
Kurama leaving Naruto in genjutsu doesn't make a bit of sense and Sakura always had good genjutsu breaking feats since part 1. Naruto lacks any gen feats in the whole manga so saying his skills in that area increased can be considered far-fetched.
As soon as Itachi activated MS he went from using Ama to gaining Shisuis crow. Itachi never tried to deploy Tsuykomi on Bee and Narutos knows exactly what Bee was capable of and told him to avoid it. Not to mention...a Perfect jin was controlled by sharigan for years.
Sasuke only needed a moment for Danzo to be in genjutsu for him to capitlize on and Rinne genjutsu is far stronger than any MS genjutsu. Ninjas are fast acting and if there senses become dulled for even a moment someone can take adv of it.